Without limiting the scope of the invention, its background is described in connection with biomarkers.
Despite advances in the fields of genomics and proteomics, a need remains for diagnostic methods and therapeutic regimens to address a large number of diseases. The fields of genomics and proteomics have served as the starting point for biological investigation as a result of the relative simplicity of their underlying subunits. In the case of genomics, scientists merely had to contend with a basic four (4) letter, linear deoxyribonucleic acid alphabet. As such, the genetic code and its determination as part of the human and other genome projects has led to vast amounts of sequence information. For proteomics, the level of complexity increases to about 20 amino acids, which are also generally linear and that are based on the underlying genetic code. Proteins have the added complexity of three-dimensional folding, with great strides in the fields of three-dimensional modeling, nuclear magnetic resonance and X-ray crystallography providing valuable tools and insight into protein structures and interaction.
Despite the sequencing of the entire human genome, large-scale gene mining operations and extensive research into the underlying causes of disease, little work has been conducted in the area of post-translational modification. The general availability of research tools may be the reason why the study of post-translational modifications has lagged behind that of the genetic code and protein expression. While the tools for determining the genetic code have been widely available for 30 years, wide spread training and availability of tools for the in-depth study of post-translational modifications, such as glycosylation, has not been generally available. The complexity of studies into post-translational modification is greatly increased by the vast numbers and complexity of the subunits, branching and even secondary modifications.
Specific examples of inventions in the general field of post-translational, glycosylation, modifications include, e.g., U.S. Pat. No. 4,659,659 issued to Dwek, et al., for a diagnostic method for diseases having an arthritic component. This patent teaches a method for the diagnosis of diseases having an arthritic component (such as rheumatoid arthritis and osteoarthritis) by determining the deficiency of galactose in a sample of the patient's blood serum or plasma, or synovial fluid, or an immunoglobulin (Ig) component or fragment thereof in comparison with the corresponding normal values of galactose. More particularly, these inventors teach a method for the diagnosis of rheumatoid arthritis or osteoarthritis as a sole syndrome or as a component of other rheumatic diseases by determining the deficiency of a single post-translational modification of a single saccharide, namely, the outer-arm galactosylation of an immunoglobulin G (IgG) component or fragment thereof in a patient's blood serum or plasma or synovial fluid by assaying for the incidence of non-reducing terminal outer arm N-acetylglucosamine residues of the IgG component or fragment and comparing with corresponding normal control values.
Another example is U.S. Reissue Pat. No. RE 35,417, issued to Rademacher, et al., which teaches oligosaccharide sequencing. More particularly, a method of oligosaccharide sequencing is taught in which the components are determined essentially simultaneously by: placing an identifying label on the reducing terminal residue of the oligosaccharide to be sequenced; dividing the oligosaccharide into a plurality of separate portions of known integer amounts; treating each the portion with a different reagent mix to thereby provide a series of reaction mixtures; pooling known integer amounts of the products from each separate reaction mixture to give a product pool; performing an analysis on the product pool which measures the molar proportions of the reaction products, and reconstructing or identifying the starting oligosaccharide from the molar prevalence of the reaction products. Again, this method relies on the sequencing of individual saccharides and is limited to a basic observational determination of the sequence without taking into account branching or other modifications.
United States Patent Application No. 20040152130, filed by Gilmore, et al., is said to teach a method for determining secondary modifications of molecules using arrays. The application provides methods for simultaneous detection of multiple secondary modifications, such as “post-translational modifications,” of target molecules, e.g., polypeptides, using an “array” format. More particularly, the method detects a secondary modification of a target molecule by: providing an array with a plurality of biosites, each biosite including a plurality of capture probes immobilized to a substrate surface; providing the target molecule; providing a detection probe capable of binding to a capture probe-bound target molecule; and, contacting the target molecule with the array and the detection probe with the target molecule and detecting which biosite comprises a bound target molecule and detection probe. Again, basic observations of the possible structure of the modification are observed without any further analysis or correlation.
Finally, United States Patent Application No. 20040067541, filed by Dwek, Miriam Victorine, et al., is directed to an assay method for the detection of detectable changes in the levels of fucosylation in Prostate Specific Antigen. An assay is taught in which a sample from a prostate suspected of being cancerous is obtained and cells and cell debris from the sample are assayed for the presence of a glycosylated protein uniquely associated with the prostate, namely, fucosylation thereof. The levels of fucosylation are compared with a standard control value indicative of a male human subject having a normal, non-cancerous prostate gland. A level of fucosylation in the sample that is statistically significantly greater than that of the control is taken as indicative of the cancerous condition.